##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:TitanCNA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings TitanCNA_1.44.0.tar.gz
###
##############################################################################
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* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/TitanCNA.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'TitanCNA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'TitanCNA' version '1.44.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'TitanCNA' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
  Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
  Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
  Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
  Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
  Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
  Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
  Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
  Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'TitanCNA'
  Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
  Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
  Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
See 'F:/biocbuild/bbs-3.20-bioc/meat/TitanCNA.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.3.0'
* checking installed package size ... NOTE
  installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data      1.7Mb
    extdata   4.9Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
computeSDbwIndex: no visible binding for global variable
  'ClonalCluster'
correctIntegerCN: no visible binding for global variable
  'Median_HaplotypeRatio'
correctIntegerCN: no visible binding for global variable 'Chromosome'
correctIntegerCN: no visible binding for global variable 'Copy_Number'
correctIntegerCN: no visible binding for global variable
  'logR_Copy_Number'
correctIntegerCN: no visible binding for global variable 'Median_logR'
correctIntegerCN: no visible binding for global variable
  'Cellular_Prevalence'
correctIntegerCN: no visible binding for global variable 'Chr'
correctIntegerCN: no visible binding for global variable 'LogRatio'
correctIntegerCN: no visible binding for global variable
  'CellularPrevalence'
correctIntegerCN: no visible binding for global variable
  'Corrected_Ratio'
correctIntegerCN: no visible binding for global variable
  'Corrected_Copy_Number'
correctIntegerCN: no visible binding for global variable
  'Corrected_Call'
correctIntegerCN: no visible binding for global variable 'TITAN_call'
correctIntegerCN: no visible binding for global variable
  'Corrected_MajorCN'
correctIntegerCN: no visible binding for global variable 'MajorCN'
correctIntegerCN: no visible binding for global variable
  'Corrected_MinorCN'
correctIntegerCN: no visible binding for global variable 'MinorCN'
correctIntegerCN: no visible binding for global variable 'CopyNumber'
correctIntegerCN: no visible binding for global variable 'TITANcall'
correctReadDepth: no visible global function definition for 'queryHits'
correctReadcount: no visible global function definition for 'loess'
correctReadcount: no visible global function definition for 'predict'
correctReadcount: no visible global function definition for 'approxfun'
correctReadcount: no visible global function definition for 'lowess'
extendSegments: no visible binding for global variable 'Start'
extendSegments: no visible binding for global variable 'End'
extendSegments: no visible binding for global variable 'Chromosome'
extendSegments: no visible binding for global variable 'Start.snp'
extendSegments: no visible binding for global variable 'End.snp'
extendSegments: no visible binding for global variable 'Start.telo'
extendSegments: no visible binding for global variable 'seq.info'
extractAlleleReadCounts: no visible global function definition for
  'PileupParam'
extractAlleleReadCounts: no visible global function definition for
  'BcfFile'
extractAlleleReadCounts: no visible global function definition for
  'scanBcf'
extractAlleleReadCounts: no visible global function definition for
  'ScanBamParam'
extractAlleleReadCounts: no visible global function definition for
  'scanBamFlag'
extractAlleleReadCounts: no visible global function definition for
  'BamFile'
extractAlleleReadCounts: no visible global function definition for
  'pileup'
extractAlleleReadCounts: no visible global function definition for
  'write.table'
getHaplotypesFromVCF: no visible global function definition for
  'rowRanges<-'
getHaplotypesFromVCF: no visible global function definition for
  'rowRanges'
getHaplotypesFromVCF: no visible global function definition for
  'na.omit'
getHaplotypesFromVCF: no visible global function definition for
  'unstrsplit'
getHaplotypesFromVCF: no visible global function definition for
  'queryHits'
getHaplotypesFromVCF: no visible global function definition for
  'DataFrame'
getOverlap: no visible global function definition for 'as'
getOverlap: no visible global function definition for 'queryHits'
getOverlap: no visible global function definition for 'subjectHits'
getPositionOverlap: no visible global function definition for 'as'
getSubcloneProfiles: no visible global function definition for
  'read.delim'
getSubcloneProfiles: no visible binding for global variable
  'CopyNumber'
getSubcloneProfiles: no visible binding for global variable 'TITANcall'
keepChr: no visible global function definition for 'as'
loadAlleleCounts: no visible global function definition for
  'read.delim'
loadBXcountsFromBEDDir: no visible binding for global variable
  'BXcounts'
loadBXcountsFromBEDDir: no visible binding for global variable 'BX'
loadBXcountsFromBEDDir: no visible global function definition for
  'RangedData'
loadHaplotypeAlleleCounts: no visible global function definition for
  'read.delim'
loadHaplotypeAlleleCounts: no visible global function definition for
  'subjectHits'
loadHaplotypeAlleleCounts: no visible global function definition for
  'as'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'phasedAlleleFraction'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'phasedCount'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'depth'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'SNPs'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'HaplotypeFraction'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'HaplotypeDepth.sum'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'HaplotypeBinDepth.sum'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'HaplotypeDepth.mean'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'HaplotypeBinDepth.mean'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'phaseSet'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'haplotypeBin'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'HaplotypeFraction.symmetric'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'HaplotypeDepth.sum.symmetric'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'HaplotypeDepth.mean.symmetric'
loadHaplotypeAlleleCounts: no visible global function definition for
  '.'
loadHaplotypeAlleleCounts: no visible global function definition for
  'na.omit'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'phasedCount.haploSymmetric'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'nonRef'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'phaseSet.aggr'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'HaplotypeRatio'
loadHaplotypeAlleleCounts: no visible binding for global variable
  'tumDepth'
loadReadCountsFromBed: no visible global function definition for
  'excludeCentromere'
loadReadCountsFromBed: no visible global function definition for
  'filterByTargetedSequences'
mergeSegsByCol: no visible binding for global variable 'Median_Ratio'
mergeSegsByCol: no visible binding for global variable 'Median_logR'
mergeSegsByCol: no visible binding for global variable 'End'
mergeSegsByCol: no visible binding for global variable 'Length.snp.'
outlierObslik: no visible global function definition for 'dunif'
outputModelParameters: no visible global function definition for
  'write.table'
outputTitanResults: no visible global function definition for
  'write.table'
outputTitanSegments: no visible binding for global variable 'Sample'
plotAllelicCN: no visible binding for global variable 'Allele.1'
plotAllelicCN: no visible binding for global variable 'LogRatio'
plotAllelicCN: no visible binding for global variable 'Allele.2'
plotAllelicCN: no visible binding for global variable 'Chr'
plotAllelicCN: no visible binding for global variable 'TITANcall'
plotAllelicCN: no visible global function definition for 'par'
plotAllelicCN: no visible binding for global variable 'CopyNumber'
plotAllelicCN: no visible global function definition for 'points'
plotAllelicCN: no visible global function definition for 'lines'
plotAllelicRatio: no visible binding for global variable 'Chr'
plotAllelicRatio: no visible binding for global variable 'TITANcall'
plotAllelicRatio: no visible global function definition for 'par'
plotAllelicRatio: no visible binding for global variable 'AllelicRatio'
plotAllelicRatio: no visible global function definition for 'lines'
plotCNlogRByChr: no visible binding for global variable 'LogRatio'
plotCNlogRByChr: no visible binding for global variable 'Median_logR'
plotCNlogRByChr: no visible binding for global variable 'Chr'
plotCNlogRByChr: no visible binding for global variable 'TITANcall'
plotCNlogRByChr: no visible global function definition for 'par'
plotCNlogRByChr: no visible global function definition for 'lines'
plotCNlogRByChr: no visible binding for global variable 'Chromosome'
plotCNlogRByChr : <anonymous>: no visible global function definition
  for 'lines'
plotCNlogRByChr: no visible binding for global variable
  'End_Position.bp.'
plotCNlogRByChr: no visible binding for global variable
  'Start_Position.bp.'
plotChrLines: no visible global function definition for 'lines'
plotChrLines: no visible global function definition for 'axis'
plotClonalFrequency: no visible binding for global variable
  'ClonalCluster'
plotClonalFrequency: no visible binding for global variable
  'CellularPrevalence'
plotClonalFrequency: no visible binding for global variable 'TITANcall'
plotClonalFrequency: no visible binding for global variable 'Chr'
plotClonalFrequency: no visible global function definition for 'par'
plotClonalFrequency: no visible global function definition for 'lines'
plotClonalFrequency: no visible global function definition for 'mtext'
plotGeneAnnotation: no visible global function definition for 'abline'
plotGeneAnnotation: no visible global function definition for 'mtext'
plotHaplotypeFraction: no visible binding for global variable
  'HaplotypeRatio.1'
plotHaplotypeFraction: no visible binding for global variable
  'HaplotypeRatio'
plotHaplotypeFraction: no visible binding for global variable
  'HaplotypeRatio.2'
plotHaplotypeFraction: no visible binding for global variable 'Chr'
plotHaplotypeFraction: no visible binding for global variable
  'TITANcall'
plotHaplotypeFraction: no visible global function definition for 'par'
plotHaplotypeFraction: no visible global function definition for
  'points'
plotHaplotypeFraction: no visible binding for global variable
  'AllelicRatio'
plotHaplotypeFraction: no visible global function definition for
  'lines'
plotIdiogram.hg38: no visible global function definition for 'par'
plotIdiogram.hg38: no visible binding for global variable 'lsegments'
plotIdiogram.hg38: no visible binding for global variable 'lpolygon'
plotIdiogram.hg38: no visible global function definition for 'axis'
plotIdiogram.hg38: no visible global function definition for 'text'
plotSegmentMedians: no visible binding for global variable 'Chromosome'
plotSegmentMedians: no visible binding for global variable 'TITAN_call'
plotSegmentMedians: no visible global function definition for 'par'
plotSegmentMedians: no visible binding for global variable
  'End_Position.bp.'
plotSegmentMedians: no visible global function definition for '.'
plotSegmentMedians: no visible binding for global variable
  'Start_Position.bp.'
plotSegmentMedians: no visible binding for global variable 'MajorCN'
plotSegmentMedians: no visible binding for global variable 'MinorCN'
plotSegmentMedians : <anonymous>: no visible global function definition
  for 'lines'
plotSegmentMedians: no visible global function definition for 'lines'
plotSegmentMedians: no visible binding for global variable
  'Copy_Number'
plotSubcloneProfiles: no visible binding for global variable 'Chr'
plotSubcloneProfiles: no visible global function definition for 'par'
plotSubcloneProfiles: no visible binding for global variable
  'CopyNumber'
plotSubcloneProfiles: no visible global function definition for 'axis'
plotSubcloneProfiles: no visible global function definition for
  'points'
plotSubcloneProfiles: no visible global function definition for 'mtext'
plotSubcloneProfiles: no visible global function definition for 'lines'
printSDbw: no visible global function definition for 'write.table'
removeCentromereSegs: no visible binding for global variable
  'Chromosome'
removeCentromereSegs: no visible binding for global variable 'Start'
removeCentromereSegs: no visible binding for global variable 'End'
removeEmptyClusters: no visible global function definition for 'tail'
runEMclonalCN: no visible binding for global variable 'head'
updateParameters: no visible global function definition for 'uniroot'
wigToRangedData: no visible global function definition for 'RangedData'
Undefined global functions or variables:
  . Allele.1 Allele.2 AllelicRatio BX BXcounts BamFile BcfFile
  CellularPrevalence Cellular_Prevalence Chr Chromosome ClonalCluster
  CopyNumber Copy_Number Corrected_Call Corrected_Copy_Number
  Corrected_MajorCN Corrected_MinorCN Corrected_Ratio DataFrame End
  End.snp End_Position.bp. HaplotypeBinDepth.mean HaplotypeBinDepth.sum
  HaplotypeDepth.mean HaplotypeDepth.mean.symmetric HaplotypeDepth.sum
  HaplotypeDepth.sum.symmetric HaplotypeFraction
  HaplotypeFraction.symmetric HaplotypeRatio HaplotypeRatio.1
  HaplotypeRatio.2 Length.snp. LogRatio MajorCN Median_HaplotypeRatio
  Median_Ratio Median_logR MinorCN PileupParam RangedData SNPs Sample
  ScanBamParam Start Start.snp Start.telo Start_Position.bp. TITAN_call
  TITANcall abline approxfun as axis depth dunif excludeCentromere
  filterByTargetedSequences haplotypeBin head lines loess
  logR_Copy_Number lowess lpolygon lsegments mtext na.omit nonRef par
  phaseSet phaseSet.aggr phasedAlleleFraction phasedCount
  phasedCount.haploSymmetric pileup points predict queryHits read.delim
  rowRanges rowRanges<- scanBamFlag scanBcf seq.info subjectHits tail
  text tumDepth uniroot unstrsplit write.table
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "mtext", "par",
             "points", "text")
  importFrom("methods", "as")
  importFrom("stats", "approxfun", "dunif", "loess", "lowess", "na.omit",
             "predict", "uniroot")
  importFrom("utils", "head", "read.delim", "tail", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... NOTE
checkRd: (-1) computeSDbwIndex.Rd:37: Lost braces; missing escapes or markup?
    37 | S_Dbw Validity Index is an internal clustering evaluation that is used for model selection (Halkidi et al. 2002). It attempts to choose the model that minimizes within cluster variances (scat) and maximizes density-based cluster separation (Dens). Then, S_Dbw(|c_{T}|x z)=Dens(|c_{T}|x z)+scat(|c_{T}|x z). 
       |                                                                                                                                                                                                                                                                        ^
checkRd: (-1) computeSDbwIndex.Rd:37: Lost braces; missing escapes or markup?
    37 | S_Dbw Validity Index is an internal clustering evaluation that is used for model selection (Halkidi et al. 2002). It attempts to choose the model that minimizes within cluster variances (scat) and maximizes density-based cluster separation (Dens). Then, S_Dbw(|c_{T}|x z)=Dens(|c_{T}|x z)+scat(|c_{T}|x z). 
       |                                                                                                                                                                                                                                                                                         ^
checkRd: (-1) computeSDbwIndex.Rd:37: Lost braces; missing escapes or markup?
    37 | S_Dbw Validity Index is an internal clustering evaluation that is used for model selection (Halkidi et al. 2002). It attempts to choose the model that minimizes within cluster variances (scat) and maximizes density-based cluster separation (Dens). Then, S_Dbw(|c_{T}|x z)=Dens(|c_{T}|x z)+scat(|c_{T}|x z). 
       |                                                                                                                                                                                                                                                                                                          ^
checkRd: (-1) computeSDbwIndex.Rd:39: Lost braces; missing escapes or markup?
    39 | In the context of \pkg{TitanCNA}, if \code{data.type}=\sQuote{\code{LogRatio}}, then the S_Dbw internal data consists of copy number log ratios, and the resulting joint states of copy number (c_{T}, forall c_{T} in \{0 : max.copy.number\}) and clonal cluster (z) make up the clusters in the internal evaluation. If \code{data.type}=\sQuote{\code{AllelicRatio}}, then the S_Dbw internal data consists of the allelic ratios. The optimal \pkg{TitanCNA} run is chosen as the run with the minimum S_Dbw. If \code{data.type}=\sQuote{\code{Both}}, then the sum of the S_Dbw for \sQuote{\code{LogRatio}} and \sQuote{\code{AllelicRatio}} are added together. This helps account for both data types when choosing the optimal solution.
       |                                                                                                                                                                                                   ^
checkRd: (-1) computeSDbwIndex.Rd:39: Lost braces; missing escapes or markup?
    39 | In the context of \pkg{TitanCNA}, if \code{data.type}=\sQuote{\code{LogRatio}}, then the S_Dbw internal data consists of copy number log ratios, and the resulting joint states of copy number (c_{T}, forall c_{T} in \{0 : max.copy.number\}) and clonal cluster (z) make up the clusters in the internal evaluation. If \code{data.type}=\sQuote{\code{AllelicRatio}}, then the S_Dbw internal data consists of the allelic ratios. The optimal \pkg{TitanCNA} run is chosen as the run with the minimum S_Dbw. If \code{data.type}=\sQuote{\code{Both}}, then the sum of the S_Dbw for \sQuote{\code{LogRatio}} and \sQuote{\code{AllelicRatio}} are added together. This helps account for both data types when choosing the optimal solution.
       |                                                                                                                                                                                                                 ^
prepare_Rd: correctCN.Rd:51-53: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: 'list'
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'plotIdiogram.hg38'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.20-bioc/R/library/TitanCNA/libs/x64/TitanCNA.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
TitanCNA-package   36.58   0.64   37.87
runEMclonalCN      29.12   0.45   31.52
TitanCNA-plotting   8.64   0.18    8.81
filterData          8.31   0.21    8.54
getPositionOverlap  7.56   0.13    7.69
computeSDbwIndex    7.07   0.14    7.20
correctReadDepth    6.61   0.18    6.79
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 WARNINGs, 5 NOTEs
See
  'F:/biocbuild/bbs-3.20-bioc/meat/TitanCNA.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL TitanCNA
###
##############################################################################
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'TitanCNA' ...
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 13.3.0'
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fwd_backC_clonalCN.c -o fwd_backC_clonalCN.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c getPositionOverlapC.c -o getPositionOverlapC.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c register.c -o register.o
gcc  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c viterbiC_clonalCN.c -o viterbiC_clonalCN.o
gcc -shared -s -static-libgcc -o TitanCNA.dll tmp.def fwd_backC_clonalCN.o getPositionOverlapC.o register.o viterbiC_clonalCN.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-TitanCNA/00new/TitanCNA/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'GenomicRanges::shift' by 'data.table::shift' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::first' by 'dplyr::first' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::desc' by 'dplyr::desc' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::slice' by 'dplyr::slice' when loading 'TitanCNA'
Warning: replacing previous import 'GenomeInfoDb::intersect' by 'dplyr::intersect' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::last' by 'dplyr::last' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::union' by 'dplyr::union' when loading 'TitanCNA'
Warning: replacing previous import 'data.table::between' by 'dplyr::between' when loading 'TitanCNA'
Warning: replacing previous import 'BiocGenerics::combine' by 'dplyr::combine' when loading 'TitanCNA'
Warning: replacing previous import 'IRanges::collapse' by 'dplyr::collapse' when loading 'TitanCNA'
Warning: replacing previous import 'GenomicRanges::setdiff' by 'dplyr::setdiff' when loading 'TitanCNA'
Warning: replacing previous import 'dplyr::select' by 'VariantAnnotation::select' when loading 'TitanCNA'
** testing if installed package keeps a record of temporary installation path
* DONE (TitanCNA)